Freesurfer July 2011

freesurfer@nmr.mgh.harvard.edu

129 participants
195 discussions

Re: [Freesurfer] Problem registering labels to native space
by John Richey 21 Jul '11

21 Jul '11

Quick update: this fix worked brilliantly. Many thanks for the help, J Richey -----Original Message----- From: Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: Monday, July 18, 2011 5:20 PM To: John Richey Cc: 'Bruce Fischl'; 'freesurfer(a)nmr.mgh.harvard.edu' Subject: Re: [Freesurfer] Problem registering labels to native space In that case, try this instead doug # Create a register.dat to fsaverage/mni305 cd $SUBJECTS_DIR/subject/mri tkregister2 --s subject --targ orig.mgz \ --ixfm transforms/talairach.xfm --zero-cras \ --reg transforms/talairach.reg.dat \ --mov $FREESURFER_HOME/subjects/fsaverage/mri/orig.mgz \ --noedit # Create a register.dat to the 2mm version of fsaverage/mni305 mri_matrix_multiply \ -im $FREESURFER_HOME/subjects/fsaverage/mri.2mm/reg.2mm.dat \ -im transforms/talairach.reg.dat \ -om transforms/mni305.2mm.reg.dat # Check tkregister2 --reg transforms/mni305.2mm.reg.dat \ --mov $FREESURFER_HOME/subjects/fsaverage/mri.2mm/orig.mgz \ --surfs # Run label2label mri_label2label --srclabel mni305.2mm.label \ --trglabel $SUBJECTS_DIR/subject/labels/mni305.2mm.label \ --regmethod volume \ --reg $SUBJECTS_DIR/subject/mri/transforms/mni305.2mm.reg.dat \ --xfm-invert John Richey wrote: > Hi Doug, this is indeed an fsfast analysis. I used the fsaverage > subject included with the 5.1 distribution. Here is the code that I > used to produce the registration matrix for one subject. Note that I > did use mri_convert to change the .mgz files into .nii.gz > > The use of flirt (below) is more of an ad-hoc solution to register > each subject's anatomical image to fsaverage. I'm not wedded to this > method if there's a better alternative. > > bet ${SUBJECTS_DIR}/${SUBJECT}/mri/nu.nii.gz \ > ${SUBJECTS_DIR}/${SUBJECT}/mri/nu_bet.nii.gz \ -f 0.3 -g 0 > > flirt -in ${SUBJECTS_DIR}/${SUBJECT}/mri/nu_bet.nii.gz \ -ref > ${SUBJECTS_DIR}/fsaverage/mri/brain.nii.gz \ -out > ${SUBJECTS_DIR}/${SUBJECT}/mri/nu_bet_reg.nii.gz \ -omat > ${SUBJECTS_DIR}/${SUBJECT}/mri/nu_bet_reg.mat \ -bins 256 -cost > corratio -searchrx -90 90 -searchry -90 90 \ -searchrz -90 90 -dof 12 > -interp trilinear > > cd $SUBJECTS_DIR > tkregister2 --targ $SUBJECTS_DIR/${SUBJECT}/mri/nu_bet_reg.nii.gz \ > --mov $SUBJECTS_DIR/fsaverage/mri/brain.nii.gz \ --fsl > $SUBJECTS_DIR/${SUBJECT}/mri/nu_bet_reg.mat \ --reg > $SUBJECTS_DIR/${SUBJECT}/mri/nu_bet_reg.dat \ --noedit > > > > -----Original Message----- > From: Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu] > Sent: Monday, July 18, 2011 3:11 PM > To: John Richey > Cc: 'Bruce Fischl'; 'freesurfer(a)nmr.mgh.harvard.edu' > Subject: Re: [Freesurfer] Problem registering labels to native space > > How did you create it? What is the actual "fsaverage space"? Is this > an FSFAST analysis? > doug > > John Richey wrote: > >> Hi Doug, the .dat file that I mention below had already been >> converted >> > into > >> a fs matrix using tkregister2. >> >> -----Original Message----- >> From: Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu] >> Sent: Monday, July 18, 2011 12:38 PM >> To: John Richey >> Cc: 'Bruce Fischl'; 'freesurfer(a)nmr.mgh.harvard.edu' >> Subject: Re: [Freesurfer] Problem registering labels to native space >> >> You can't use a flirt matrix with mri_label2label. You can convert a >> flirt matrix to the proper format with tkregister2 using the --fsl >> option (this will allow you to check the reg as well). >> >> doug >> >> John Richey wrote: >> >> >>> Hi Bruce, >>> >>> The labels that I have fsaverage space are 3D/volume-based and not >>> surface-based labels. >>> >>> >>> -----Original Message----- >>> From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] >>> Sent: Monday, July 18, 2011 12:00 PM >>> To: John Richey >>> Cc: 'freesurfer(a)nmr.mgh.harvard.edu' >>> Subject: RE: [Freesurfer] Problem registering labels to native space >>> >>> Hi John >>> >>> why are you using an affine volume registration for fsaverage? Why >>> not use surface registration? >>> >>> Bruce >>> >>> >>> On Mon, 18 Jul 2011, John Richey wrote: >>> >>> >>> >>> >>>> Hi Bruce - thanks for the reply. >>>> >>>> Here is my command line: >>>> >>>> mri_label2label --srcsubject fsaverage \ --trgsubject ${SUBJECT} >>>> --srclabel $SUBJECTS_DIR/group_analysis/${CONTRAST}/${LABEL} \ >>>> --trglabel $SUBJECTS_DIR/${SUBJECT}/label/${CONTRAST}_${LABEL} \ >>>> --regmethod volume \ --reg $SUBJECTS_DIR/$SUBJECT/mri/brain_reg.dat >>>> >>>> Where "brain_reg.dat" is the subject-specific matrix I created >>>> through FLIRT. However, as I mentioned, disincluding this matrix >>>> does not seem to change the result much. >>>> >>>> One other problem I encounter... Occasionally when I view the >>>> label in native space, the label itself seems to be eroded on a >>>> voxel-wise >>>> >>>> >>>> >>> basis. >>> >>> >>> >>>> That is, the label essentially appears as a series of >>>> non-contiguous dots (which if dialated would become contiguous). >>>> >>>> >>>> >>>> >>>> >>>> >>>> -----Original Message----- >>>> From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] >>>> Sent: Monday, July 18, 2011 11:20 AM >>>> To: John Richey >>>> Cc: 'freesurfer(a)nmr.mgh.harvard.edu' >>>> Subject: Re: [Freesurfer] Problem registering labels to native >>>> space >>>> >>>> Hi John >>>> >>>> can you email us your label2label cmdline? >>>> >>>> cheers >>>> Bruce >>>> >>>> >>>> On Mon, 18 Jul 2011, John Richey >>>> wrote: >>>> >>>> >>>> >>>> >>>>> Dear freesurfer experts, >>>>> >>>>> I have a series of labels corresponding to clusters of significant >>>>> activation in fsaverage space. >>>>> >>>>> I want to map these back to native space using mri_label2label, >>>>> however when I view the individual (native) labels, the >>>>> registration is way off and the labels do not map into plausible space. >>>>> >>>>> I have tried using talairach space as an intemediary (by omitting >>>>> the --reg flag in mri_label2label), as well as using fsl tools >>>>> (FLIRT) to create a registration matrix but unfortunately I cannot >>>>> seem to get the label into the right space to query my ces maps in >>>>> >>>>> >> funcroi-sess. >> >> >>>>> Have others encountered this problem? And how might I create a >>>>> more robust registration between fsaverage and native space to >>>>> facilitate the spatial transformation of my labels? >>>>> >>>>> Thanks very much in advance, >>>>> John >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>> The information in this e-mail is intended only for the person to >>>> whom it is addressed. If you believe this e-mail was sent to you in >>>> error and the e-mail contains patient information, please contact >>>> the Partners Compliance HelpLine at >>>> http://www.partners.org/complianceline >>>> . If the e-mail was sent to you in error but does not contain >>>> patient information, please contact the sender and properly dispose >>>> of the >>>> >>>> >> e-mail. >> >> >>>> >>>> >>>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> >>> >>> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve(a)nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> >> >> >> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

1 0

Segmentation Fault during mri_ca_normalize
by Tali Swisher 21 Jul '11

21 Jul '11

Hi all, I was having consistent errors with two cases during mri_ca_normalize, and after using an updated version (mri_ca_normalize_centos), one case went through smoothly. I'm having trouble with the second case, however; it now repeatedly reports a segmentation fault partway through mri_ca_normalize (error message below) - any ideas?? Thanks! Tali Swisher #@# CA Normalize Thu Jul 21 12:25:47 EDT 2011 /home/pnlstaff/freesurfer/subjects/umd_V2_20110711/mri mri_ca_normalize -mask brainmask.mgz nu.mgz /share/apps/freesurfer4.0.5/average/RB_all_2008-03-26.gca transforms/talairach.lta norm.mgz using MR volume brainmask.mgz to mask input volume... reading 1 input volumes reading atlas from '/share/apps/freesurfer4.0.5/average/RB_all_2008-03-26.gca'... reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... resetting wm mean[0]: 102 --> 107 resetting gm mean[0]: 64 --> 64 input volume #1 is the most T1-like using real data threshold=19.0 using (122, 88, 141) as brain centroid... mean wm in atlas = 107, using box (106,72,120) --> (137, 104,162) to find MRI wm before smoothing, mri peak at 215 after smoothing, mri peak at 214, scaling input intensities by 0.500 scaling channel 0 by 0.5 using 244171 sample points... INFO: compute sample coordinates transform 1.134 0.005 0.006 -38.602; 0.006 1.132 0.138 -19.653; 0.004 -0.150 1.048 -20.038; 0.000 0.000 0.000 1.000; INFO: transform used finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (142, 46, 61) --> (202, 147, 218) Left_Cerebral_White_Matter: limiting intensities to 97.0 --> 111.0 19 of 76 (25.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (87, 48, 60) --> (144, 148, 219) Right_Cerebral_White_Matter: limiting intensities to 95.0 --> 107.0 27 of 73 (37.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (146, 122, 85) --> (188, 161, 136) Left_Cerebellum_White_Matter: limiting intensities to 92.0 --> 105.0 5 of 18 (27.8%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (103, 122, 83) --> (144, 160, 137) Right_Cerebellum_White_Matter: limiting intensities to 95.0 --> 108.0 0 of 7 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (130, 115, 118) --> (158, 176, 147) Segmentation fault Linux compute-2-1.local 2.6.9-34.ELsmp #1 SMP Fri Feb 24 16:56:28 EST 2006 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Thu Jul 21 12:28:18 EDT 2011 -- Talis M. Swisher, BA Research Assistant Psychiatry Neuroimaging Laboratory Harvard Medical School, Brigham and Women's Hospital 1249 Boylston St, 3rd Floor Boston, MA 02215 Office: (617) 525-6119 Cell: (336) 577-5071 Fax: (617) 525-6150

2 1

literature about multiple comparison correction
by Tetiana Dadakova 21 Jul '11

21 Jul '11

Dear list, Could you please recommend the literature about multiple comparisons correction, especially about Monte-Carlo simulation. Thank you, Tanja.

3 2

Re: [Freesurfer] Calculate WM, GM and CSF volume
by Fellhauer, Iven 21 Jul '11

21 Jul '11

Hi Bruce, Yes, I would like to reduce the required calculation time, until desired results are available. Best regards, Iven -----Ursprüngliche Nachricht----- Von: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Gesendet: Mittwoch, 20. Juli 2011 15:19 An: Fellhauer, Iven Cc: freesurfer(a)nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] Calculate WM, GM and CSF volume Hi Iven, is there a reason you don't want to just run recon-all -all? It's more time for the computer, but no more for you and will give you a lot more measures cheers Bruce On Wed, 20 Jul 2011, Fellhauer, Iven wrote: > Dear All, > > I want to calculate the volume of WM, GM and CSF. First of all I have converted the .mri files to .mgz files. I have checked the ReconAllDevTable page to get the recon-all switches to calculate the volume of GM, WM and CFS. > > I want to use the following switches to calculate the volume, but I' m not sure if this works/is right: > recon-all -autorecon1 - gcareg -canorm -careg -rmneck -skull-lta > -calabel -segstatts -subject <subject> > > Did I miss something? Is there a better/faster way to get/calculate the volumes? The command returns the correct results? > > Best regards, > > Iven Fellhauer > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

2 1

Tracula with individual bvecs files
by Jürgen Hänggi 21 Jul '11

21 Jul '11

Dear FS and Tracula experts Because of correction for slice angulation during scanning, I have as many bvecs files as subjects. Therefore I created a list for the bvecs set bvecslist = (b101/bvecs b102/bvecs) but tracula reports the following error: mv: rename /Users/juergenhaenggi/Desktop/Tracula/Results/b101/dmri/dwi_orig_flip.mghdti .bvecs to /Users/juergenhaenggi/Desktop/Tracula/Results/b101/dmri/bvecs: No such file or directory However, when using set bvecsfile, everthing works fine. Any idea how to deal with more than one bvecs file? Thanks in advance Regards Jürgen ---------------------------------------------------------------------------- Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ----------------------------------------------------------------------------

2 1

re-running recon-all failing
by Satrajit Ghosh 20 Jul '11

20 Jul '11

hi all, i'm trying to rerun some subjects processed with 5.0 with 5.1 and am getting the following error on all the subjects. simply executing recon-all -s subjid -all any ideas? cheers, satra ---------- unfolding failed - restoring original position -------------------- 0750: dt=0.001250, rms=0.380 (0.000%), neg=0, invalid=766 writing output transformation to transforms/talairach.m3z... GCAMwrite GCAMwrite:: m3z loop GCAMwrite:: the command is: gzip -f -c > transforms/talairach.m3z registration took 4 hours, 1 minutes and 50 seconds. ERROR: mri_ca_register with non-zero status 1 but continuing despite the error #-------------------------------------- #@# CA Reg Inv Mon Jul 18 14:54:53 EDT 2011 /g2/users/satra/TESTCVS/surfaces/ek041bk/mri mri_ca_register -invert-and-save transforms/talairach.m3z Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z zcat transforms/talairach.m3z Inverting GCAM Saving inverse ERROR: mri_ca_register with non-zero status 0

2 2

tksurfer image rendering error
by Martina Ly 20 Jul '11

20 Jul '11

Hello freesurfer community, I am viewing an inflated image generated by tksurfer using the command: tksurfer "subjid" rh inflated The image appears to have rendering issues only on certain workstations (Mac OS X 10.6.5) but works on other linux machines. The shading doesn't have high resolution (low resolution gradients, appears to be 8bit). I've attached a photo. I am accessing the data locally and the video card driver (ATI) has been updated. I've also tried entering: export doublebufferflag=1. Any help or suggestions would be greatly appreciated! Best, Martina

2 1

ROI analysis with label in both hemispheres
by Katie Bettencourt 20 Jul '11

20 Jul '11

Hi all, I was wondering if anyone had any idea if it was possible to combine together ROIs from the separate hemispheres into one ROI (for example LH V1 and RH V1) and then perform a functional ROI analysis on it. I know how to combine ROIs (through labels_union) and how to do a functional ROI analysis (using func2roi-sess and roisummary-sess), but I don't know if it is possible to do it with a label that runs across both hemispheres. Thoughts? Thanks, Katie

1 0

Multiecho sequences available for Siemens
by Brian C. Schweinsburg, Ph.D. 20 Jul '11

20 Jul '11

Hi Folks, I noticed in the multiecho portion of the freesurfer wiki that it says custom multiecho sequences are available from Martinos for use. I was wondering who I might contact for information on obtaining sequences for our 3T Siemens scanner as I hoped to test these out with freesurfer. Thanks, Brian

2 1

Contrast with two covariates in conjunction?
by Gonzalo Sanchez Benavides 20 Jul '11

20 Jul '11

Dear Freesurfers, I'm exploring the relationship among cortical thickness, aging and some cognitive variables in a sample of healthy elders, and I want to test this relationship regardless sex and years of education. I think is easy to make contrasts to explore separately the correlation between age (or a cognitive measure) and thickness. However I am wondering if its possible to know the areas in which both correlations coincide. Does it make sense to use a contrast like this for such purpose? 0 0 0.5 0.5 0 0 0.5 0.5 sex age edu cognitive measure Many thanks in advance for your answer -- Gonzalo Sánchez Benavides

2 1

← Newer
1
...
4
5
6
7
8
9
10
...
20
Older →

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer July 2011